Hmm, well, there are some aesthetic differences given what version you buy (i.e. the color of the stat bar in battle is white in White 2 and the location pop-ups is black in Black 2). Like in BW1, Opelucid City will look different between Black 2 and White 2, as will Mistralton City and Route 4. Finally some locations have different layouts and one location even switches around puzzles.
Also, White 2 gives you the option to get Reshiram while Black 2 affords the opportunity to get Zekrom (I am guessing to help make up for what you don't get in BW1).
The story, so far as I know, remains the same; and as with all versions the Pokemon available will differ.
For those interested, here's the version exclusive PKMN listings courtesy of Serebii:
http://www.serebii.net/black2white2/exclusives.shtmland...in case anyone is curious about the details of aesthetic and layout changes (caution that the links may contain spoilers about the storyline, so don't say I didn't warn you)
[spoiler9zu](The In-Battle/Location Pop-Up Aesthetic Differences and Unova Link Differences courtesy of Serebii)
http://www.serebii.net/black2white2/versionmisc.shtml (The Layout changes and City Aesthetics Differences, also courtesy of Serebii)
http://www.serebii.net/black2white2/versionarea.shtml[/spoiler9zu]